THE PHILIPPINES and Indonesia will jointly patrol the Celebes Sea this week to stop Islamist militants reaching the Philippines' restive southern island of Mindanao, where rebels have seized a city, an army spokesman said on Sunday.

The joint patrol is aimed at strengthening border security and improving interoperability, military spokesman Major Ezra Balagtey said in a statement. The two countries' warships will sail from the Philippines' Davao city on Thursday.

"The coordinated patrol ... is intended to strengthen the security of the Davao Gulf and the common boundary of the two countries in the southern archipelago, particularly along the Celebes Sea," said Balagtey.

Regional governments fear fighters sympathetic to the Islamic State group will cross maritime borders from Malaysia and Indonesia to join rebels who seized Marawi City five weeks ago.

About 300 militants, 82 members of the Philippines' security force and 44 civilians have been killed in fighting.

The coordinated patrol is the third in the region in a month as pirates and militants step up attacks on commercial shipping.

The Philippines was joined by the United States on Saturday to patrol southern Philippine waters. Two weeks ago, Indonesia, Malaysia and the Philippines jointly patrolled their common maritime borders in the Celebes Sea and Sulu Sea.

The latest patrol will end next week in the Indonesian city of Manado on Sulawesi island.